1 Introduction

This paper contains estimates for the effective reproduction number \(R_{t,m}\) over time \(t\) in various countries \(m\) of the world. This is done using the methodology as described in [1]. These have been implemented in R using EpiEstim package [2] which is what is used here. The methodology and assumptions are described in more detail here.

This paper and it’s results should be updated roughly daily and is available online.

As this paper is updated over time this section will summarise significant changes. The code producing this paper is tracked using Git. The Git commit hash for this project at the time of generating this paper was 5bede93abdb36f8e6d27c4fefe65f76d78d4af53.

2 Data

Data are downloaded from [3]. Minor formatting is applied to get the data ready for further processing.

3 Basic Exploration

Below cumulative case count is plotted on a log scale by continent.

Cumulative Reported Cases by Continent

Cumulative Reported Cases by Continent

Below a 7-day moving average of daily case count is plotted on a log scale by continent.

Daily Reported Cases by Continent (7-day moving average)

Daily Reported Cases by Continent (7-day moving average)

Below cumulative deaths by country is plotted on a log scale:

Cumulative Reported Deaths by Continent

Cumulative Reported Deaths by Continent

Below a 7-day moving average of daily deaths by country is plotted on a log scale:

Daily Deaths by Continent (7-day moving average)

Daily Deaths by Continent (7-day moving average)

4 Method & Assumptions

The methodology is described in detail here.

Countries with populations of less than 500 000 are excluded.

5 Results

5.1 World-wide

Estimated Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
cases 5,502,898 2021-04-20 1.1 1.1 1.1
deaths 84,797 2021-04-20 1.0 1.0 1.0

5.2 Current reproduction number estimates by country

Below current (last weekly) \(R_{t,m}\) estimates are plotted on a world map.

5.2.0.1 Cases

5.2.1 Deaths

5.3 Top 10 countries

Below we show various extremes of \(R_{t,m}\) where counts (deaths or cases) exceed 50 in the last week.

5.3.1 Lowest \(R_{t,m}\) based on deaths

Country Estimated Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
Honduras deaths 103 2021-04-20 0.5 0.6 0.7
Mexico deaths 2,766 2021-04-20 0.5 0.6 0.7
Philippines deaths 855 2021-04-20 0.6 0.7 0.7
Spain deaths 477 2021-04-20 0.6 0.7 0.8
Yemen deaths 65 2021-04-20 0.6 0.7 0.9
Sudan deaths 93 2021-04-20 0.6 0.8 0.9
Estonia deaths 55 2021-04-20 0.6 0.8 1.0
Czechia deaths 602 2021-04-20 0.7 0.8 0.9
North America deaths 8,641 2021-04-20 0.8 0.8 0.8
Italy deaths 2,545 2021-04-20 0.8 0.8 0.9

5.3.2 Lowest \(R_{t,m}\) based on cases

Country Estimated Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
Djibouti cases 480 2021-04-20 0.5 0.6 0.6
Rwanda cases 402 2021-04-20 0.6 0.6 0.7
Malawi cases 96 2021-04-20 0.5 0.6 0.8
Ghana cases 299 2021-04-20 0.6 0.7 0.8
Albania cases 1,090 2021-04-20 0.6 0.7 0.7
El Salvador cases 1,035 2021-04-20 0.6 0.7 0.8
Bangladesh cases 29,795 2021-04-20 0.7 0.7 0.8
Botswana cases 1,258 2021-04-20 0.7 0.7 0.8
Hungary cases 26,755 2021-04-20 0.7 0.7 0.8
Mali cases 1,067 2021-04-20 0.7 0.8 0.8

5.3.3 Highest \(R_{t,m}\) based on deaths

Country Estimated Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
India deaths 10,468 2021-04-20 1.4 1.5 1.7
Oman deaths 111 2021-04-20 1.2 1.5 1.8
Qatar deaths 51 2021-04-20 1.0 1.4 1.9
Iran deaths 2,470 2021-04-20 1.3 1.4 1.5
Cuba deaths 62 2021-04-20 1.0 1.3 1.7
Guatemala deaths 222 2021-04-20 1.1 1.3 1.5
Japan deaths 260 2021-04-20 1.1 1.3 1.5
Asia deaths 21,098 2021-04-20 1.2 1.3 1.3
Kosovo deaths 101 2021-04-20 1.0 1.3 1.6
Colombia deaths 2,695 2021-04-20 1.2 1.3 1.3

5.3.4 Highest \(R_{t,m}\) based on cases

Country Estimated Type Count (Last Week) Week Ending R - Lower CI R - Mean R - Uppper CI
Nepal cases 6,583 2021-04-20 1.9 2.1 2.3
Equatorial Guinea cases 286 2021-04-20 1.5 1.9 2.5
Trinidad and Tobago cases 624 2021-04-20 1.5 1.7 1.9
Gambia cases 182 2021-04-20 1.3 1.6 1.8
Thailand cases 10,610 2021-04-20 1.4 1.5 1.7
Suriname cases 324 2021-04-20 1.3 1.5 1.7
Cambodia cases 2,748 2021-04-20 1.4 1.5 1.6
Sudan cases 1,250 2021-04-20 1.2 1.4 1.7
Zimbabwe cases 545 2021-04-20 1.3 1.4 1.5
India cases 1,742,305 2021-04-20 1.3 1.4 1.5

5.4 Risk Quadrants

The plots below show weekly cases (or deaths) on the X-axis and the reproduction number on the Y-axis. By dividing this into 4 quadrants we can identify countries with high cases and high reproduction numbers, or high cases and low reproduction numbers etc.

Values where the reproduction number exceeds 3 are plotted at 3.

5.4.1 Cases

Risk Quadrants - Cases

5.4.2 Deaths

Risk Quadrants - Deaths

5.5 Country Plots by Continent

Below we plot results for each country/province in a list. Values larger than 3 are plotted at 3.

5.5.1 Africa

5.5.1.1 Algeria

5.5.1.2 Angola

5.5.1.3 Benin

5.5.1.4 Botswana

5.5.1.5 Burkina Faso

5.5.1.6 Burundi

5.5.1.7 Cameroon

5.5.1.8 Cape Verde

5.5.1.9 Central African Republic

5.5.1.10 Chad

5.5.1.11 Comoros

5.5.1.12 Congo

5.5.1.13 Cote d’Ivoire

5.5.1.14 Democratic Republic of Congo

5.5.1.15 Djibouti

5.5.1.16 Egypt

5.5.1.17 Equatorial Guinea

5.5.1.18 Eritrea

5.5.1.19 Eswatini

5.5.1.20 Ethiopia

5.5.1.21 Gabon

5.5.1.22 Gambia

5.5.1.23 Ghana

5.5.1.24 Guinea

5.5.1.25 Guinea-Bissau

5.5.1.26 Kenya

5.5.1.27 Lesotho

5.5.1.28 Liberia

5.5.1.29 Libya

5.5.1.30 Madagascar

5.5.1.31 Malawi

5.5.1.32 Mali

5.5.1.33 Mauritania

5.5.1.34 Mauritius

5.5.1.35 Morocco

5.5.1.36 Mozambique

5.5.1.37 Namibia

5.5.1.38 Niger

5.5.1.39 Nigeria

5.5.1.40 Rwanda

5.5.1.41 Senegal

5.5.1.42 Sierra Leone

5.5.1.43 Somalia

5.5.1.44 South Africa

5.5.1.45 South Sudan

5.5.1.46 Sudan

5.5.1.47 Togo

5.5.1.48 Tunisia

5.5.1.49 Uganda

5.5.1.50 Zambia

5.5.1.51 Zimbabwe

5.5.2 Asia

5.5.2.1 Afghanistan

5.5.2.2 Armenia

5.5.2.3 Azerbaijan

5.5.2.4 Bahrain

5.5.2.5 Bangladesh

5.5.2.6 Bhutan

5.5.2.7 Cambodia

5.5.2.8 China

5.5.2.9 Georgia

5.5.2.10 India

5.5.2.11 Indonesia

5.5.2.12 Iran

5.5.2.13 Iraq

5.5.2.14 Israel

5.5.2.15 Japan

5.5.2.16 Jordan

5.5.2.17 Kazakhstan

5.5.2.18 Kuwait

5.5.2.19 Kyrgyzstan

5.5.2.20 Lebanon

5.5.2.21 Malaysia

5.5.2.22 Maldives

5.5.2.23 Mongolia

5.5.2.24 Myanmar

5.5.2.25 Nepal

5.5.2.26 Oman

5.5.2.27 Pakistan

5.5.2.28 Palestine

5.5.2.29 Philippines

5.5.2.30 Qatar

5.5.2.31 Saudi Arabia

5.5.2.32 Singapore

5.5.2.33 South Korea

5.5.2.34 Sri Lanka

5.5.2.35 Syria

5.5.2.36 Taiwan

5.5.2.37 Tajikistan

5.5.2.38 Thailand

5.5.2.39 Timor

5.5.2.40 Turkey

5.5.2.41 United Arab Emirates

5.5.2.42 Uzbekistan

5.5.2.43 Vietnam

5.5.2.44 Yemen

5.5.3 Europe

5.5.3.1 Albania

5.5.3.2 Austria

5.5.3.3 Belarus

5.5.3.4 Belgium

5.5.3.5 Bosnia and Herzegovina

5.5.3.6 Bulgaria

5.5.3.7 Croatia

5.5.3.8 Cyprus

5.5.3.9 Czechia

5.5.3.10 Denmark

5.5.3.11 Estonia

5.5.3.12 Finland

5.5.3.13 France

5.5.3.14 Germany

5.5.3.15 Greece

5.5.3.16 Hungary

5.5.3.17 Ireland

5.5.3.18 Italy

5.5.3.19 Kosovo

5.5.3.20 Latvia

5.5.3.21 Lithuania

5.5.3.22 Luxembourg

5.5.3.23 Moldova

5.5.3.24 Montenegro

5.5.3.25 Netherlands

5.5.3.26 North Macedonia

5.5.3.27 Norway

5.5.3.28 Poland

5.5.3.29 Portugal

5.5.3.30 Romania

5.5.3.31 Russia

5.5.3.32 Serbia

5.5.3.33 Slovakia

5.5.3.34 Slovenia

5.5.3.35 Spain

5.5.3.36 Sweden

5.5.3.37 Switzerland

5.5.3.38 Ukraine

5.5.3.39 United Kingdom

5.5.4 North America

5.5.4.1 Canada

5.5.4.2 Costa Rica

5.5.4.3 Cuba

5.5.4.4 Dominican Republic

5.5.4.5 El Salvador

5.5.4.6 Guatemala

5.5.4.7 Haiti

5.5.4.8 Honduras

5.5.4.9 Jamaica

5.5.4.10 Mexico

5.5.4.11 Nicaragua

5.5.4.12 Panama

5.5.4.13 Trinidad and Tobago

5.5.4.14 United States

5.5.5 Oceania

5.5.5.1 Australia

5.5.5.2 New Zealand

5.5.5.3 Papua New Guinea

5.5.6 South America

5.5.6.1 Argentina

5.5.6.2 Bolivia

5.5.6.3 Brazil

5.5.6.4 Chile

5.5.6.5 Colombia

5.5.6.6 Ecuador

5.5.6.7 Guyana

5.5.6.8 Paraguay

5.5.6.9 Peru

5.5.6.10 Suriname

5.5.6.11 Uruguay

5.5.6.12 Venezuela

5.6 Detailed Output

Detailed output for all countries are saved to a comma-separated value file. The file can be found here.

6 Discussion

Limitation of this method to estimate \(R_{t,m}\) are noted in [1]

  • It’s sensitive to changes in transmissibility, changes in contact patterns, depletion of the susceptible population and control measures.
  • It relies on an assumed generation interval assumptions.
  • The size of the time window can affect the volatility of results.
  • Results are time lagged with regards to true infection, more so in the case of the use of deaths.
  • It’s sensitive to changes in case (or death) detection.
  • The generation interval may change over time.

Further to the above the estimates are made under assumption that the cases and deaths are reported consistently over time. For cases this means that testing needs to be at similar levels and reported with similar lag. Should these change rapidly over an interval of a few weeks the above estimates of the effective reproduction numbers would be biased. For example a rapid expansion of testing over the last 3 weeks would results in overestimating recent effective reproduction numbers. Similarly any changes in reporting (over time and underreporting) of deaths would also bias estimates of the reproduction number estimated using deaths.

Estimates for the reproduction number are plotted in time period in which the relevant measure is recorded. Though in reality the infections giving rise to those estimates would have occurred roughly between a week to 4 weeks earlier depending on whether it was cases or deaths. These figures have not been shifted back.

Despite these limitation we believe the ease of calculation of this method and the ability to use multiple sources makes it useful as a monitoring tool.

7 Author

This report was prepared by Louis Rossouw. Please get in contact with Louis Rossouw if you have comments or wish to receive this regularly.

Louis Rossouw
Head of Research & Analytics
Gen Re | Life/Health Canada, South Africa, Australia, NZ, UK & Ireland
Email: LRossouw@GenRe.com Mobile: +27 71 355 2550

The views in this document represents that of the author and may not represent those of Gen Re. Also note that given the significant uncertainty involved with the parameters, data and methodology care should be taken with these numbers and any use of these numbers.

References

[1] A. Cori, N. M. Ferguson, C. Fraser, and S. Cauchemez, “A new framework and software to estimate time-varying reproduction numbers during epidemics,” American Journal of Epidemiology, vol. 178, no. 9, pp. 1505–1512, Sep. 2013, doi: 10.1093/aje/kwt133. [Online]. Available: https://doi.org/10.1093/aje/kwt133

[2] A. Cori, EpiEstim: A package to estimate time varying reproduction numbers from epidemic curves. 2013 [Online]. Available: https://CRAN.R-project.org/package=EpiEstim

[3] M. Roser, H. Ritchie, E. Ortiz-Ospina, and J. Hasell, “Coronavirus pandemic (COVID-19),” Our World in Data, 2020 [Online]. Available: https://ourworldindata.org/coronavirus. [Accessed: 17-Dec-2020]